Snake Eater's gameplay is similar to that of previous games in the Metal Gear Solid series. Snake, controlled by the player, must move undetected through a hostile, enemy-filled environment. Although Snake acquires various weapons (ranging from handguns to rocket propelled grenades), the emphasis is on using stealth to avoid confrontations. A number of objects and gadgets can be found along the way to aid in this, including motion detectors to track hostile soldiers, and the Metal Gear series' trademark cardboard box, which Snake can hide under to avoid visual detection. Despite the fundamental similarities, Snake Eater introduces many new aspects of gameplay not present in previous Metal Gear games, including camouflage, a new hand-to-hand combat system called "close-quarters combat" or "CQC", a stamina gauge, and an injury-and-treatment system.
Approximately two-thirds of the game is set outdoors in a fictional Soviet Union rain forest, and using this varied environment to its fullest potential is often the key to success. Of the new features, particular emphasis is placed on camouflage and using the jungle environment itself (for example, climbing trees or hiding in tall grass) to avoid being seen by the enemy. The advanced radar from previous games has been removed in favor of a simple motion detector and sonar system more suitable for Snake Eater's time period.
A percentage value called the "camouflage index" displays Snake's visibility, on a scale from negative values (highly visible) up to 100% (completely invisible to the enemy). In order to minimize visibility, the player must switch between different camouflage uniforms and face paints to blend in with the environment; for example, wearing a bark-patterned uniform while leaning against a tree, or wearing striped face paint while hiding in tall grass.
The basic close combat from previous installments has been heavily refined and expanded into the CQC system. When unarmed or using a one-handed weapon, Snake can grab opponents and put them in a chokehold, at which point a variety of actions can be performed, such as choking the enemy unconscious or interrogating them at knifepoint to obtain information.
While previous games used only a simple life bar, Snake Eater also keeps track of injuries over the entire body. For example, a long fall could fracture Snake's leg, slowing him down until the injury is properly treated with a splint and bandage. Unless these injuries are treated, Snake will not be able to fully recover his health for some time.
The location brings in the need to rely upon native flora and fauna to survive. This is manifested in a stamina gauge, which constantly depletes during gameplay. Failure to restore the gauge by eating has detrimental effects on gameplay, such as decreasing Snake's ability to aim his weapon. Food can be stored in the backpack until it is needed. However, some types of food rot over time, and consuming rotten foods may result in Snake developing a stomach ache, causing the stamina gauge to deplete faster